Man pages for andrewparkermorgan/popcorn
File-Format Wrangler for Population-Based Genetic Data

dot-fix_sexEncode sex as integer
dot-prep.layoutdraw the characteristic TreeMix tree with migration edges
dot-sort_indivInternal helper function for sorting rows in ADMIXTURE...
myldplyA 'dplyr'-friendly equivalent to the old 'plyr::ldply()'
pca_vcfPerform PCA on a VCF file using 'akt pca' and consume result
plot_admixtureMake standard stacked-bars plot of ancestry proportions.
plot_treemixPlot population tree
read_beagle_ibdRead BEAGLE-format IBD segments
read_bedRead genomic intervals in BED format
read_coverageRead output from my '' script
read_famRead a PLINK family (*.fam) file
read_het_plinkRead estimated inbreeding report from PLINK
read_homozyg_plinkRead ROH report from PLINK
read_loglik_filesRead log-likelihoods from ADMIXTURE runs
read_mapRead a PLINK marker map (*.bim) file
read_Q_matrixRead ancestry proportions ('Q-matrix') from ADMIXTURE run
read_rohRead 'bcftools roh' output (mode '-Or")
read_treemixRead TreeMix output files
scale_comboCombined shape and colour scale for uniquely identifying many...
scale_shape_repeaterDiscrete scale of different point shapes that repeats
sort_by_clusterSort samples by admixture components using crude heuristics
theme_admixtureA ggplot theme for ADMIXTURE plots
theme_niceClean-looking ggplot2 theme, similar to 'theme_classic()'
theme_slanty_xMake ggplot2 x-axis labels slanted
theme_treemixPlotting theme for TreeMix population trees
tidyConvert admixture proportions to tidy format.
andrewparkermorgan/popcorn documentation built on May 25, 2019, 2:25 p.m.